The simplest way is to run from flash.
To do so, first compile and build your project. If all goes well, in your Build Console (should be the window at the bottom of your screen if you didn't touch it) will report that <Project Name>.out file was successfully built. If not, that means that there are errors in your code or something is wrong...
Assuming that that's good, go to Window->Preferences...
From there, go to the tab that says FIRST Downloader Preferences and input your team number and find the .out file you just created. It should be under workspace/<project folder>/PPC603/Debug... (something like that)
Once you find it press OK to save your preferences...
Assuming that your cRIO is connected and you're getting communication on your DSU (should read battery voltage), make sure your IP settings are correct on your computer.
If that's good, go to FIRST->Download and wait for your program to send.
Reboot your cRIO when you're done and wait for communication again.
Flip the toggle on your DSU to Enable and it should work...